scholarly journals Molecular Mechanism ofN,N-Dimethylformamide Degradation inMethylobacteriumsp. Strain DM1

2019 ◽  
Vol 85 (12) ◽  
Author(s):  
Xinyu Lu ◽  
Weiwei Wang ◽  
Lige Zhang ◽  
Haiyang Hu ◽  
Ping Xu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Gene Clusters ◽  
Sole Source ◽  
Human Beings ◽  
Sequencing Data ◽  
Carbon And Nitrogen ◽  
Redundant Genes ◽  
Evolutionary Advantage ◽  
Redundant Gene ◽  
Phenotype Identification

ABSTRACTN,N-Dimethylformamide (DMF) is one of the most common xenobiotic chemicals, and it can be easily emitted into the environment, where it causes harm to human beings. Herein, an efficient DMF-degrading strain, DM1, was isolated and identified asMethylobacteriumsp. This strain can use DMF as the sole source of carbon and nitrogen. Whole-genome sequencing of strain DM1 revealed that it has a 5.66-Mbp chromosome and a 200-kbp megaplasmid. The plasmid pLVM1 specifically harbors the genes essential for the initial steps of DMF degradation, and the chromosome carries the genes facilitating subsequent methylotrophic metabolism. Through analysis of the transcriptome sequencing data, the complete mineralization pathway and redundant gene clusters of DMF degradation were elucidated. The dimethylformamidase (DMFase) gene was heterologously expressed, and DMFase was purified and characterized. Plasmid pLVM1 is catabolically crucial for DMF utilization, as evidenced by the phenotype identification of the plasmid-free strain. This study systematically elucidates the molecular mechanisms of DMF degradation byMethylobacterium.IMPORTANCEDMF is a hazardous pollutant that has been used in the chemical industry, pharmaceutical manufacturing, and agriculture. Biodegradation as a method for removing DMF has received increasing attention. Here, we identified an efficient DMF degrader,Methylobacteriumsp. strain DM1, and characterized the complete DMF mineralization pathway and enzymatic properties of DMFase in this strain. This study provides insights into the molecular mechanisms and evolutionary advantage of DMF degradation facilitated by plasmid pLVM1 and redundant genes in strain DM1, suggesting the emergence of new ecotypes ofMethylobacterium.

scholarly journals Catabolism of 3-hydroxypyridine by Ensifer adhaerens HP1: a novel four-component gene encoding 3-hydroxypyridine dehydrogenase HpdA catalyzes the first step of biodegradation

2020 ◽  
Author(s):  
Haixia Wang ◽  
Xiaoyu Wang ◽  
Hao Ren ◽  
Xuejun Wang ◽  
Zhenmei Lu
Keyword(s):  
Gene Cluster ◽  
Microbial Degradation ◽  
Molecular Mechanisms ◽  
Gene Clusters ◽  
Sole Source ◽  
Pyridine Derivative ◽  
Gene Encoding ◽  
Ensifer Adhaerens ◽  
Important Building Block ◽  
Component Gene

Abstract3-Hydroxypyridine (3HP) is an important natural pyridine derivative. Ensifer adhaerens HP1 can utilize 3HP as the sole source of carbon, nitrogen and energy to grow. However, the genes responsible for the degradation of 3HP remain unknown. In this study, we predicted that a gene cluster, designated 3hpd, may be responsible for the degradation of 3HP. The initial hydroxylation of 3HP is catalyzed by a four-component dehydrogenase (HpdA1A2A3A4), leading to the formation of 2,5-dihydroxypyridine (2,5-DHP) in E. adhaerens HP1. In addition, the SRPBCC component in HpdA existed as a separate subunit, which is different from other SRPBCC-containing molybdohydroxylases acting on N-heterocyclic aromatic compounds. Our findings provide a better understanding of the microbial degradation of pyridine derivatives in nature. Additionally, research on the origin of the discovered four-component dehydrogenase with a separate SRPBCC domain may be of great significance.Importance3-Hydroxypyridine is an important building block for synthesizing drugs, herbicides and antibiotics. Although the microbial degradation of 3-hydroxypyridine has been studied for many years, the molecular mechanisms remain unclear. Here, we show that 3hpd is responsible for the catabolism of 3-hydroxypyridine. The 3hpd gene cluster was found to be widespread in Actinobacteria, Rubrobacteria, Thermoleophilia, and Alpha-, Beta-, and Gammaproteobacteria, and the genetic organization of the 3hpd gene clusters in these bacteria showed high diversity. Our findings provide new insight into the catabolism of 3-hydroxypyridine in bacteria.

scholarly journals Genes of theN-Methylglutamate Pathway Are Essential for Growth of Methylobacterium extorquens DM4 with Monomethylamine

2014 ◽  
Vol 80 (11) ◽  
pp. 3541-3550 ◽  
Author(s):  
Christelle Gruffaz ◽  
Emilie E. L. Muller ◽  
Yousra Louhichi-Jelail ◽  
Yella R. Nelli ◽  
Gilles Guichard ◽  
...  
Keyword(s):  
Carbon Source ◽  
Nitrogen Source ◽  
Gene Clusters ◽  
Sole Source ◽  
Nadh:Ubiquinone Oxidoreductase ◽  
Methylotrophic Bacteria ◽  
Methylobacterium Extorquens ◽  
Content Type ◽  
Carbon And Nitrogen ◽  
In The Wild

ABSTRACTMonomethylamine (MMA, CH3NH2) can be used as a carbon and nitrogen source by many methylotrophic bacteria.Methylobacterium extorquensDM4 lacks the MMA dehydrogenase encoded bymaugenes, which inM. extorquensAM1 is essential for growth on MMA. Identification and characterization of minitransposon mutants with an MMA-dependent phenotype showed that strain DM4 grows with MMA as the sole source of carbon, energy, and nitrogen by theN-methylglutamate (NMG) pathway. Independent mutations were found in a chromosomal region containing the genesgmaS,mgsABC, andmgdABCDfor the three enzymes of the pathway, γ-glutamylmethylamide (GMA) synthetase, NMG synthase, and NMG dehydrogenase, respectively. Reverse transcription-PCR confirmed the operonic structure of the two divergent gene clustersmgsABC-gmaSandmgdABCDand their induction during growth with MMA. The genesmgdABCDandmgsABCwere found to be essential for utilization of MMA as a carbon and nitrogen source. The genegmaSwas essential for MMA utilization as a carbon source, but residual growth of mutant DM4gmaSgrowing with succinate and MMA as a nitrogen source was observed. Plasmid copies ofgmaSand thegmaShomolog METDI4690, which encodes a protein 39% identical to GMA synthetase, fully restored the ability of mutants DM4gmaSand DM4gmaSΔmetdi4690 to use MMA as a carbon and nitrogen source. Similarly, chemically synthesized GMA, the product of GMA synthetase, could be used as a nitrogen source for growth in the wild-type strain, as well as in DM4gmaSand DM4gmaSΔmetdi4690 mutants. The NADH:ubiquinone oxidoreductase respiratory complex component NuoG was also found to be essential for growth with MMA as a carbon source.

scholarly journals In-depth transcriptomic analysis of human retina reveals molecular mechanisms underlying diabetic retinopathy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kolja Becker ◽  
Holger Klein ◽  
Eric Simon ◽  
Coralie Viollet ◽  
Christian Haslinger ◽  
...  
Keyword(s):  
Diabetic Retinopathy ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Vision Loss ◽  
Ganglion Cells ◽  
Expression Profiles ◽  
Cell Types ◽  
Sequencing Data ◽  
Disease Stages ◽  
Post Transcriptional Regulation

AbstractDiabetic Retinopathy (DR) is among the major global causes for vision loss. With the rise in diabetes prevalence, an increase in DR incidence is expected. Current understanding of both the molecular etiology and pathways involved in the initiation and progression of DR is limited. Via RNA-Sequencing, we analyzed mRNA and miRNA expression profiles of 80 human post-mortem retinal samples from 43 patients diagnosed with various stages of DR. We found differentially expressed transcripts to be predominantly associated with late stage DR and pathways such as hippo and gap junction signaling. A multivariate regression model identified transcripts with progressive changes throughout disease stages, which in turn displayed significant overlap with sphingolipid and cGMP–PKG signaling. Combined analysis of miRNA and mRNA expression further uncovered disease-relevant miRNA/mRNA associations as potential mechanisms of post-transcriptional regulation. Finally, integrating human retinal single cell RNA-Sequencing data revealed a continuous loss of retinal ganglion cells, and Müller cell mediated changes in histidine and β-alanine signaling. While previously considered primarily a vascular disease, attention in DR has shifted to additional mechanisms and cell-types. Our findings offer an unprecedented and unbiased insight into molecular pathways and cell-specific changes in the development of DR, and provide potential avenues for future therapeutic intervention.

scholarly journals Screening for the Production and Characterization of L-asparaginase from Endophytic Fungi

2021 ◽  
Vol 8 (5) ◽  
pp. 168-173
Author(s):  
Harjeet Singh ◽  
Shweta Sao
Keyword(s):  
Lymphoblastic Leukemia ◽  
Fungal Endophytes ◽  
Erwinia Carotovora ◽  
Maximum Activity ◽  
Phenol Red ◽  
Human Beings ◽  
Ph Indicator ◽  
Carbon And Nitrogen ◽  
Sds Page ◽  
Secondary Neoplasm

L-asparaginase (EC 3.5.11. L-asparagine amidohydrolase) is first enzyme, studied very intensively in human beings with regard to its anti-tumor potential against tumor of lymphoid precursor, acute lymphoblastic leukemia (ALL). The current drugs are suffering from many side effects like immune suppression, infertility, secondary neoplasm. The immunogenic complications associated with its present microbial sources Escherichia coli; Erwinia carotovora limits its medicinal frontier. So there exists a need of switching to novel natural sources to serve as non-immunogenic and better production sources of L-asparaginase. In the present study, four cultures of fungal endophytes viz. TSF-1, TSF-2, TSF-3 and TSF-4 selected on the basis of primary and secondary screening was carried on with L-asparagine as a sole carbon and nitrogen source and phenol red as pH indicator. The maximum protein content was observed to be present in TSF-2 i.e. 2.727 mg /mL and possessed maximum activity of 6.054 Units/ml. Sample was separated by SDS-PAGE, stained by silver staining, showed a single band with molecular weight of approximately ~45kDa.

scholarly journals Amino Acid-Mediated Induction of the Basic Amino Acid-Specific Outer Membrane Porin OprD from Pseudomonas aeruginosa

1999 ◽  
Vol 181 (17) ◽  
pp. 5426-5432 ◽  
Author(s):  
Martina M. Ochs ◽  
Chung-Dar Lu ◽  
Robert E. W. Hancock ◽  
Ahmed T. Abdelal
Keyword(s):  
Amino Acids ◽  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Regulatory Protein ◽  
Basic Amino Acid ◽  
Sole Source ◽  
Activation Mechanism ◽  
Beta Lactam ◽  
Mobility Shift ◽  
Carbon And Nitrogen

ABSTRACT Pseudomonas aeruginosa can utilize arginine and other amino acids as both carbon and nitrogen sources. Earlier studies have shown that the specific porin OprD facilitates the diffusion of basic amino acids as well as the structurally analogous beta-lactam antibiotic imipenem. The studies reported here showed that the expression of OprD was strongly induced when arginine, histidine, glutamate, or alanine served as the sole source of carbon. The addition of succinate exerted a negative effect on induction ofoprD, likely due to catabolite repression. The arginine-mediated induction was dependent on the regulatory protein ArgR, and binding of purified ArgR to its operator upstream of theoprD gene was demonstrated by gel mobility shift and DNase assays. The expression of OprD induced by glutamate as the carbon source, however, was independent of ArgR, indicating the presence of more than a single activation mechanism. In addition, it was observed that the levels of OprD responded strongly to glutamate and alanine as the sole sources of nitrogen. Thus, that the expression ofoprD is linked to both carbon and nitrogen metabolism ofPseudomonas aeruginosa.

scholarly journals Identification of Key Regulators of Hepatitis C Virus-Induced Hepatocellular Carcinoma by Integrating Whole-Genome and Transcriptome Sequencing Data

2021 ◽  
Vol 12 ◽  
Author(s):  
Guolin Chen ◽  
Wei Zhang ◽  
Yiran Ben
Keyword(s):  
Hepatocellular Carcinoma ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Molecular Mechanisms ◽  
Sequencing Data ◽  
Regulatory Pathways ◽  
Regulatory Module ◽  
Carcinogenic Potential ◽  
Potential Biomarker ◽  
New Biomarkers

Background: Hepatitis C virus (HCV) infection is a major cause of cirrhosis and hepatocellular carcinoma (HCC). Despite recent advances in the understanding of the biological basis of HCC development, the molecular mechanisms underlying HCV-induced HCC (HCC-HCV) remain unclear. The carcinogenic potential of HCV varies according to the genotype and mutation in its viral sequence. Moreover, regulatory pathways play important roles in many pathogenic processes. Therefore, identifying the pathways by which HCV induces HCC may enable improved HCC diagnosis and treatment.Methods: We employed a systematic approach to identify an important regulatory module in the process of HCV-HCC development to find the important regulators. First, an HCV-related HCC subnetwork was constructed based on the gene expression in HCC-HCV patients and HCC patients. A priority algorithm was then used to extract the module from the subnetworks, and all the regulatory relationships of the core genes of the network were extracted. Integrating the significantly highly mutated genes involved in the HCC-HCV patients, core regulatory modules and key regulators related to disease prognosis and progression were identified.Result: The key regulatory genes including EXO1, VCAN, KIT, and hsa-miR-200c-5p were found to play vital roles in HCV-HCC development. Based on the statistics analysis, EXO1, VCAN, and KIT mutations are potential biomarkers for HCV–HCC prognosis at the genomic level, whereas has-miR-200c-5P is a potential biomarker for HCV–HCC prognosis at the expression level.Conclusion: We identified three significantly mutated genes and one differentially expressed miRNA, all related to HCC prognosis. As potential pathogenic factors of HCC, these genes and the miRNA could be new biomarkers for HCV-HCC diagnosis.

Blood Transcriptome Analysis reveals Age-associated changes in Expression Profile of Immune-Related Gene in Golden snub-nosed Monkey(Rhinopithecus roxellana)

2019 ◽  
Author(s):  
Shao Huanhuan ◽  
Deng Jiabo ◽  
Wu Linfeng ◽  
Li Xuedan ◽  
Niu Lili ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Cell Activity ◽  
Young Group ◽  
Functional Enrichment ◽  
Rhinopithecus Roxellana ◽  
Sequencing Data ◽  
Adult Group ◽  
New Genes ◽  
Age Related ◽  
Differential Genes

Abstract Background Golden snub-nosed monkeys ( Rhinopithecus roxellana ) are an endangered species in China.In the present study, the blood transcriptomes of nine monkeys were characterized by using RNA-Seq technology.Results 57.31 Gb high-quality sequencing data was obtained. The clean data of each sample was >5 Gb, and 86.17% to 94.48% of the reads of each sample could be compared to reference genome of snub-nosed monkey. After assembly, we obtained 24,992 genes, including 3,917 new genes. Many genes were up-regulated or down-regulated with age. In adult group of R. roxellana roxellana, there were 76 differential genes, including 68 up-regulated and 8 down-regulated genes, compared with the young group. While, compared with the adult group, in the old group there were 58 differential genes, including 25 up-regulated genes and 23 down-regulated genes. In R. roxellana qinlingensis , compared with the young group, 117 differential genes were obtained, including 34 up-regulated and 83 down-regulated genes. Functional enrichment analysis indicated that the up-regulated genes were mainly related to innate immune response and T-cell activity, while the down-regulated genes were mainly involved in B-cell activity, suggesting that immune competence of adult group increased gradually compared to young group. However, the adaptive immune function declined gradually in the old group.Conclusions Our findings will contribute to understand on the molecular mechanisms of age-related changes in immune system, which will provide a foundation for future study in snub-nosed monkey.

Abstract 14532: Computational Drug Repurposing Identifies a Piperlongumine Analog That Controls a Gstp1-iscu Pathogenic Axis in Pulmonary Hypertension

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Jimin Yang
Keyword(s):  
Drug Repurposing ◽  
Gene Clusters ◽  
Loss Of Function ◽  
Sequencing Data ◽  
Glutathione S Transferase ◽  
Computational Screening ◽  
Therapeutic Development ◽  
Pulmonary Arterial

Background and Hypothesis: Pulmonary arterial hypertension (PAH) is an incurable vascular disease for which chemotherapies are being considered for therapeutic development. There is no method reported to date for effective computational screening of these drugs for this disease. Big data analyses that leverage the molecular parallels between cancer and PH may define novel pathogenic mechanisms and facilitate repurposing of chemotherapies for PAH. More specifically, while functional deficiency of the iron-sulfur (Fe-S) biogenesis gene ISCU and oxidative metabolism in human pulmonary arterial endothelial cells (PAECs) is known to drive PAH, the pathogenic regulation of ISCU is not fully defined, and no tailored drugs have been identified to bolster ISCU activity. Methods and Results: We applied a computational algorithm EDDY (Evaluating Differential DependencY), which analyzes RNA sequencing data from 810 cancer cell lines exposed to 368 small molecules, in order to identify chemotherapeutics that depended upon rewired PH-related gene clusters. The top ranked drug was a piperlongumine (PL) analog (BRD2889) that was predicted to extensively rewire dependencies across PH gene clusters, mediated by ISCU. In vitro, coupling gain- and loss-of-function analyses of GSTP1 with BRD2889 exposure in PAECs, we found that BRD2889 inhibits glutathione S-transferase P1 (GSTP1), an enzyme which in turn catalyzes ISCU glutathionylation and increases its stability in hypoxia. Consequently, BRD2889 and GSTP1 knockdown phenocopy one another by increasing Fe-S-dependent Complex I activity and mitochondrial oxygen consumption while ameliorating pathogenic apoptosis. Consistent with these computational and in vitro results, in a mouse model of PAH (IL-6 transgenic mice in hypoxia), BRD2889 improved hemodynamic and molecular disease manifestations in vivo. Conclusions: Using a novel computational platform, we identified a coordinated connection between BRD342289 and GSTP1-ISCU axis, crucial to PAEC metabolism. This study offers insight to fundamental PH pathobiology and sets the stage for accelerated repurposing of chemotherapies such as BRD342289 in PH.

scholarly journals Immunological pathways of macrophage response to Brucella ovis infection

2020 ◽  
Vol 26 (7) ◽  
pp. 635-648
Author(s):  
Zhixiong Zhou ◽  
Guojing Gu ◽  
Yichen Luo ◽  
Wenjie Li ◽  
Bowen Li ◽  
...  
Keyword(s):  
Immune Response ◽  
Molecular Mechanisms ◽  
Group Versus ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Sequencing Data ◽  
Brucella Ovis ◽  
Qrt Pcr ◽  
Raw264.7 Macrophage

As the molecular mechanisms of Brucella ovis pathogenicity are not completely clear, we have applied a transcriptome approach to identify the differentially expressed genes (DEGs) in RAW264.7 macrophage infected with B. ovis. The DEGs related to immune pathway were identified by Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) functional enrichment analysis. Quantitative real-time PCR (qRT-PCR) was performed to validate the transcriptome sequencing data. In total, we identified 337 up-regulated and 264 down-regulated DEGs in B. ovis-infected group versus mock group. Top 20 pathways were enriched by KEGG analysis and 20 GO by functional enrichment analysis in DEGs involved in the molecular function, cellular component, and biological process and so on, which revealed multiple immunological pathways in RAW264.7 macrophage cells in response to B. ovis infection, including inflammatory response, immune system process, immune response, cytokine activity, chemotaxis, chemokine-mediated signaling pathway, chemokine activity, and CCR chemokine receptor binding. qRT-PCR results showed Ccl2 (ENSMUST00000000193), Ccl2 (ENSMUST00000124479), Ccl3 (ENSMUST00000001008), Hmox1 (ENSMUST00000005548), Hmox1 (ENSMUST00000159631), Cxcl2 (ENSMUST00000075433), Cxcl2 (ENSMUST00000200681), Cxcl2 (ENSMUST00000200919), and Cxcl2 (ENSMUST00000202317). Our findings firstly elucidate the pathways involved in B. ovis-induced host immune response, which may lay the foundation for revealing the bacteria–host interaction and demonstrating the pathogenic mechanism of B. ovis.

scholarly journals E proteins orchestrate dynamic transcriptional cascades implicated in the suppression of the differentiation of group 2 innate lymphoid cells

2020 ◽  
Vol 295 (44) ◽  
pp. 14866-14877
Author(s):  
Vincent Peng ◽  
Constantin Georgescu ◽  
Anna Bakowska ◽  
Aneta Pankow ◽  
Liangyue Qian ◽  
...  
Keyword(s):  
Protein Function ◽  
Molecular Mechanisms ◽  
Innate Lymphoid Cells ◽  
Lymphoid Cells ◽  
Microbial Pathogens ◽  
Loss Of Function ◽  
Sequencing Data ◽  
E Proteins ◽  
Down Regulation ◽  
Group 2

Group 2 innate lymphoid cells (ILC2s) represent a subset of newly discovered immune cells that are involved in immune reactions against microbial pathogens, host allergic reactions, as well as tissue repair. The basic helix-loop-helix transcription factors collectively called E proteins powerfully suppress the differentiation of ILC2s from bone marrow and thymic progenitors while promoting the development of B and T lymphocytes. How E proteins exert the suppression is not well understood. Here we investigated the underlying molecular mechanisms using inducible gain and loss of function approaches in ILC2s and their precursors, respectively. Cross-examination of RNA-seq and ATAC sequencing data obtained at different time points reveals a set of genes that are likely direct targets of E proteins. Consequently, a widespread down-regulation of chromatin accessibility occurs at a later time point, possibly due to the activation of transcriptional repressor genes such as Cbfa2t3 and Jdp2. The large number of genes repressed by gain of E protein function leads to the down-regulation of a transcriptional network important for ILC2 differentiation.

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